Experiment: 7T0H

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OKD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.15 M Potassium Bromide, 30% PEG MME 2000, 5 mM 4-O-methoxymethyl-KdoOMe

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.593	α = 90
b = 63.135	β = 99.36
c = 61.885	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2015-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	OTHER	0.9795

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.3	40	99.4	0.057	0.067	0.036	13	3.7		103442

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	99.4		0.547	0.641	0.331	0.807		3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3OKD	1.3	40	90448	4735	91.41	0.151	0.1484	0.15	0.2003	0.2	RANDOM	18.319

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.04		-0.19	0.07		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.572
r_dihedral_angle_4_deg	21.138
r_sphericity_free	18.506
r_dihedral_angle_3_deg	14.371
r_sphericity_bonded	9.492
r_dihedral_angle_1_deg	7.64
r_rigid_bond_restr	7.431
r_angle_refined_deg	2.995
r_angle_other_deg	1.406
r_chiral_restr	0.211

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.572
r_dihedral_angle_4_deg	21.138
r_sphericity_free	18.506
r_dihedral_angle_3_deg	14.371
r_sphericity_bonded	9.492
r_dihedral_angle_1_deg	7.64
r_rigid_bond_restr	7.431
r_angle_refined_deg	2.995
r_angle_other_deg	1.406
r_chiral_restr	0.211
r_bond_refined_d	0.036
r_gen_planes_refined	0.018
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3341
Nucleic Acid Atoms
Solvent Atoms	592
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.